Genes & development最新文献

Platinum-based compounds and ultraviolet (UV) irradiation produce bulky DNA lesions that stall RNA polymerase II (RNAPII), activating transcription-coupled nucleotide excision repair (TC-NER), RNAPII degradation, and global transcriptional shutdown. However, the consequences of RNAPII bypassing such lesions remain unclear. We identified the acetyltransferase p300 as a key regulator of TC-NER-dependent RNAPII removal from damaged chromatin via a USP7-dependent mechanism. Loss of p300 permits RNAPII to bypass transcription-blocking lesions, sustaining transcription and full-length mRNA production despite DNA damage. This leads to continued translation, endoplasmic reticulum (ER) stress, and activation of the unfolded protein response (UPR), compromising cell viability. Notably, this stress response resensitizes tumors resistant to platinum-based chemotherapy. Our findings reveal a vulnerability in tumor cells that evade transcriptional shutdown and define a synthetic lethal interaction between p300 inhibition and platinum-induced DNA damage, offering a targeted strategy to overcome chemoresistance.

Mechanisms driving the increase in cell growth in developing leukemia are not fully understood. We focused on epigenomic regulation of this process by analyzing the changes of chromatin marks and gene expression in leukemic cell clones as they progressed toward increased proliferation in a mouse model of acute myeloid leukemia (AML). This progression was characterized by gradual modulation of chromatin states and gene expression across the genome, with a surprising preferential trend of reversing the prior changes associated with the origins of leukemia. Our analyses of this modulation in independently developing clones predicted a small set of potential growth regulators whose transcriptomic and epigenomic progression was consistent between clones and maintained both in vivo and ex vivo. We selected three of these genes as candidates (Irx5 and Plag1 as growth suppressors and Smad1 as a driver) and successfully validated their causal growth effects by overexpression in mouse leukemic cells. Overexpression of the IRX5 gene in human MOLM13 leukemic cells suppressed cell growth both in vitro and in mouse xenografts. Public patient data confirmed expression levels of PLAG1 and SMAD1 as markers of AML status and survival, suggesting that multiomic analysis of evolving clones in a mouse model is a valuable predictive approach relevant to human AML.

Mature microRNAs are generated in a series of sequential processing steps, creating multiple opportunities for regulatory bottlenecks. In this issue of Genes & Development, Shang and colleagues (doi:10.1101/gad.353316.125) dissect microRNA biogenesis by cluster assistance in human cells, demonstrating that ERH and SAFB2 have distinct functions in the processing of suboptimal hairpins. Beyond resolving the mechanistic dependencies on ERH and SAFB2, the study demonstrates that cluster assistance has been co-opted into a feedback mechanism to regulate DGCR8 levels and Microprocessor stability, elevating cluster assistance from a descriptive phenomenon to a physiologically integrated miRNA regulatory pathway.

Nuclear receptors (NRs) are ligand-regulated transcription factors (TFs) that respond to hormonal, nutritional, and environmental signals. NRs as druggable targets are known for their therapeutic potential in treating a wide range of diseases, including metabolic disorders, inflammatory conditions, and various cancers. Due to their structure and ability to interact with DNA, ligands, and other proteins, NR transcriptional regulatory capacity is fine-tuned through dynamic interactions with a disparate array of coregulators, including coactivators and corepressors that form an intricate network that integrates multiple signaling and metabolic pathways. This review synthesizes insights into the functional interactions between NRs and the modulators of transcription, focusing on interactions between NRs and coregulators and how their model of interaction has evolved from a binary switch to a coregulator shift mechanism in regulating ligand-dependent transcription. These nuanced multifaceted interactions collectively direct dynamic gene expression by NRs across multiple tissues in physiology and diseases.

Metabolism requires precise gene regulation to balance energy intake and expenditure for an organism's well-being, with misregulation often leading to metabolic syndromes. This study reveals that the brain-specific microRNA miR-1000 regulates fat storage by controlling the expression of a neuropeptide gene, Nplp1 Loss of miR-1000 increases Nplp1 expression, leading to higher body weight, increased fat storage, improved survival under food deprivation conditions, and a reduced overall life span in Drosophila We further show that miR-1000 promotes fat storage upon feeding by regulating triacylglyceride (TAG) synthesis and storage in lipid droplets, thereby playing a crucial role in metabolic regulation.

Mutations that impact maturation of human telomerase RNA (hTR) are common in telomere biology disorders. Here, we describe sequential posttranscriptional modifications that coordinate hTR biogenesis and decay. Initially, TGS1-mediated 5'-cap trimethylation targets long genomically extended hTR precursors for degradation. Prevention of 5'-cap trimethylation results in accumulation of nucleolar 3'-end extended precursors, evading MTR4 recognition and degradation by the exosome. In a second step, 3'-end oligoadenylation by PAPD5 promotes degradation of mature hTR, a process that remains dependent on 5'-cap modifications, as prevention of trimethylation inhibits decay of heavily 3'-end oligoadenylated molecules. Combined inhibition of 5'-cap trimethylation and 3'-end oligoadenylation synergistically increases hTR in cells harboring pathogenic mutations in telomerase. These data reveal a precise interplay between 5'- and 3'-end posttranscriptional modifications that dictate hTR fate and highlight the potential of RNA therapeutics for treatment of telomere biology disorders.

Retrotransposon mobilization in germline cells enables the rewriting of genetic information to drive genome innovation, species evolution, and adaptation through the generation of de novo mutations. However, uncontrolled mobilization can cause DNA breaks and genome instability, often leading to sterility. How retrotransposon mobilization that can be retained for genome evolution persists despite negative outcomes of retrotransposon activity remains poorly understood. Here, we used Drosophila spermatogenesis as a model to investigate retrotransposon mobilization dynamics. Although many retrotransposon families are transcriptionally active, we found that the LTR retrotransposon nomad completes the full mobilization cascade (including mRNA export, protein translation, and reverse transcription) to produce double-stranded DNA (dsDNA) the most efficiently. Strikingly, despite successfully generating dsDNA, nomad rarely achieves genomic reintegration. Instead, its newly synthesized DNA predominantly forms extrachromosomal circular DNA (ecDNA). These findings show that retrotransposon-derived DNA largely remains as ecDNA. This could prevent widespread genomic integration during spermatogenesis, potentially preserving genome stability with the presence of limited retrotransposon activity.

While most conserved microRNA (miRNA) transcripts harbor a suite of features that mediate their efficient biogenesis into small RNAs, some loci bear suboptimal attributes that enable additional layers of processing regulation. A notable example is cluster assistance, whereby a miRNA hairpin with suboptimal nuclear biogenesis can be enhanced by an optimal neighbor. This process involves local transfer of the Microprocessor complex, composed of the RNase III enzyme Drosha and its partner, DGCR8, in concert with cofactors such as ERH and SAFB1/2. However, the mechanisms that underlie miRNA cluster assistance remain largely unclear. Here, we gained insights into this process by integrating mutant cells of Microprocessor and its cofactors with analysis of miRNA structure-function variants, biochemical tests, and genome-wide profiling. We defined features of suboptimal miRNAs that render them dependent on cluster assistance and distinguished among a network of proposed interactions among Microprocessor and its cofactors to reveal a subset that is critical for cluster assistance. Most importantly, we used epistatic tests to separate and order the functional requirements for ERH and SAFB1/2 into a pathway. Our data indicate that ERH may engage in the process of Microprocessor transfer between hairpins, while SAFB factors (especially SAFB2) mediate recognition and stable binding of a suboptimal miRNA hairpin after Microprocessor transfer. Finally, we show how cluster assistance integrates into a feedback regulatory loop on Microprocessor via Drosha-mediated cleavage of a suboptimal miRNA hairpin in the DGCR8 transcript. Altogether, our findings reveal complex regulatory transactions during biogenesis of clustered miRNAs.

Translation elongation defects activate the integrated stress response (ISR), but whether and how ribosome stalls are cleared to enable mRNA release for ribonucleoprotein (RNP) granule assembly remain unclear. We show that blocking tRNA aminoacylation generates persistent uncollided ribosome stalls that inhibit stress granule and P-body assembly despite robust ISR activation. Collided ribosomes are rapidly cleared by ZNF598-dependent ribosome-associated quality control within 4 h, while uncollided stalls resist clearance and persist for >16 h. Puromycin releases persistent stalls and restores RNP granule formation. The block in stress granule assembly is generalizable across tRNA synthetase inhibitors and amino acid deprivation. Therefore, stress granules represent signal integrators reporting translation elongation status when initiation is suppressed. Our findings reveal that translation quality control pathways selectively clear collided ribosomes, establish that translation elongation stress uncouples RNP granule assembly from the ISR, and suggest that tolerating uncollided stalls may be adaptive for cotranslational processes essential for cellular function.